Diversity of 16S-rRNA and nifH genes derived from rhizosphere soil and roots of an endemic drought tolerant grass, Lasiurus sindicus

Lasiurus sindicus is a highly nutritive, drought tolerant, perennial grass, endemic to the Thar Desert of Rajasthan, India. In order to characterize the diversity of bacteria associated with roots of this grass that had survived severe drought stress, 16S-rRNA gene clone libraries were established from RT-PCR amplified products of the total RNA extracted from the washed roots and rhizosphere soil samples. Eight major bacterial taxa were identified in a total of 121 16S-rRNA gene clones. The majority of sequences belonged to Gram-positive bacteria, Actinobacteria being the most predominant ones, closely followed by Firmicutes. Most of the sequences showed similarity with sequences from cultivated bacteria or uncultivated environmental clones associated with arid, semi-arid environments, cold deserts and contaminated soils. PCR amplification of nifH genes using total DNA as template produced a total of 48 nifH clones from the rhizosphere soil and root samples and revealed a predominance of nifH sequences closely affiliated to Pseudomonas pseudoalcaligenes, isolated in a previous study from root samples of Lasiurus sindicus. Some nifH sequences showed close similarity to cultivated diazotrophs like Azospirillum brasilense, Rhizobium sp., and a variety of uncultured nitrogen fixing bacteria. Thus, this study provides us with evidence that L. sindicus harbors a diversity of bacteria with potential for nitrogen fixation.